Release v0.6.3

Bugfix

• Python dependencies are defined now in a more flexible way using the compatibility operator ~=, this was causing trouble to deploy in bioconda due to missing bugfix versions in conda-forge

Release v0.3.1

Release equivalent to v0.3.0, this one should come out with a DOI for referencing this software.

Release v0.6.2

Changes

• Set less strict dependencies to numpy, pandas and scipy

Release 0.6.1

Major Changes

• The annotation of neoantigen candidates from mouse are supported
• Uniprot instead of ensembl is now used to create the proteome databse

Minor Changes

• Post-translational modified peptides in the IEDB database will not be parsed
• Validation layers of the models have been refactored
• Reference versions are tracked now

Comments on mouse support

• the following features are not supported for mouse: MixMHCpred, MixMHC2pred, PHBR-I, PHBR-II, Recogntion potential, PRIME, Hex
• homozygous MHC alleles need to be provided twice also for mouse

Release v0.5.3

This is a minor release that fixes a bug introduced in v0.5.2. external annotation were not added in the released version but are added now.

Release v0.5.2

This is a minor release 0.5.2

• fix of the documenation
• estimate features such as pathogensimilarity, IEDB immunogenicity for the best MHC II peptide
• removal of the neoantigen id from the neoantigen model

Release v0.5.1

This is a minor relase, covering the following points:

• update of README
• integration of HEX

Known issues:

• HEX: the b-score is not supported in this version. The code will be transformed into python in one of the next releases. Then, the B-score will be supported aswell.
• The documentation is broken and needs to be fixed.

Release Neofox v0.5.0

Neofox v0.5.0 release notes

Major changes

• Update to NetMHCpan 4.1
• Update to NetMHCIIpan 4.0
• Integrate PRIME (Schmidt et al, 2021) as an additional feature
• Ambiguous MHC allele representations are resolved now using IMGT/HLA database
• Support for a more flexible mutation model not requiring the wild type sequence
• Generator rate for alternatively defined neoepitopes (Rech et al, 2018) is included for MHC-I and MHC-II
• Extended support for Python 3.6, 3.7 and 3.8

Minor changes

• The neoantigen unique identifier is removed from the tabular output
• The order of columns in the tabular output is changed to improve readability
• The affinity threshold is now a parameter (--affinity-threshold) with default value 500000 nM (ie: virtually disabled)
• Queries to the proteome are optimised

Bugfixes

• Best MHC alleles from MixMHCpred and MixMHC2pred are now normalized
• Logs in the file are now complete
• Avoid crashes with rare (ie: O, U) or non existing (ie: B, J, X, Z) amino acids

Known issues

• When the provided wild type sequence does not match the wild type in the proteome the best epitope may not overlap the mutation. This may occur when the wild type was derived from other proteome database than Ensembl GRCh37 or when the wild type sequence contains a germline mutation. This request takes care of the first point. Regarding the second point, the proteome database should be chosen more flexible. Internally, we will change to uniprot in the next release.
• Due to hits in the WT proteome search, a limited amount of neoepitopes or none may be left after this filtering step. For instance, this can lead to the fact that all features related to 9mers will be NA as no 9mer neoepitope candidate is present.
• Rare amino acids (ie: O and U) are returned as X by netMHCpand and netMHCIIpan

Neofox v0.4.2

Merge branch 'release-0.4.2' into 'master'

Release 0.4.2 to master

See merge request tron/addannot!132

Neofox v0.4.1

Bugfixes:

• Library distributed version was not specified and it was causing some incompatibility with latest version from December
• Documentation was pointing to an old DOI